Well to give an example of why someone might purposely throw out their case...
My game collection has grown so large that I simply don't have the space to store all my game boxes anymore. So since a few years ago I've started throwing away the boxes after a few months. The discs then go into a large CD/DVD multi-case and the manuals go into a seperate cardboard box. Once they go into 'the box' though I'd never dream of trading/selling them. IMO it just wouldn't be proper, as they're no longer 'complete'.
As for accidentally 'losing' boxes and manuals, you might be surprised just how disorganized and careless some people can be with their stuff. I know some people in real life who are a great example of this. When they get a new game, they insert the disc into the PC/console and then toss the box aside. The box usually gets buried under a heap of other junk. When they have to take out the disc because they want to put in something else, they simply put the disc down on the PC/TV/table, etc. It just gets left there until needed again.
By the time they might look for the box it's probably already been taken out with the trash. Still, these are the same kind of people who will poke around inside their PC with a screw driver because a bent DVD has become stuck in the DVD-ROM drive. So I think you get the idea... *rolls eyes*